Variant report

Variant	rs303018
Chromosome Location	chr6:25139026-25139027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr6:25138331-25139625	GM12878	blood:	n/a	chr6:25139524-25139538 chr6:25139527-25139536 chr6:25139363-25139371 chr6:25139366-25139389 chr6:25139526-25139535 chr6:25139188-25139199 chr6:25138559-25138566 chr6:25139182-25139193
2	MYC	chr6:25138377-25139321	MCF10A-Er-Src	breast:	n/a	n/a
3	SMC3	chr6:25138280-25139036	Hela-S3	cervix:	n/a	n/a
4	IRF1	chr6:25138540-25139435	K562	blood:	n/a	chr6:25139183-25139197 chr6:25139185-25139199 chr6:25139177-25139198 chr6:25139188-25139201 chr6:25139189-25139199 chr6:25139182-25139193 chr6:25139188-25139199 chr6:25139181-25139192 chr6:25139187-25139201 chr6:25139187-25139198 chr6:25139182-25139195 chr6:25139182-25139195 chr6:25139181-25139201 chr6:25139182-25139195 chr6:25139187-25139200 chr6:25139183-25139193 chr6:25139182-25139196 chr6:25139183-25139200 chr6:25139186-25139200 chr6:25139188-25139200 chr6:25139189-25139203 chr6:25139182-25139195 chr6:25139179-25139193
5	POLR2A	chr6:25138179-25139227	SK-N-SH	brain:	n/a	n/a
6	MTA3	chr6:25137947-25139435	GM12878	blood:	n/a	n/a
7	IRF1	chr6:25138938-25139384	K562	blood:	n/a	chr6:25139183-25139197 chr6:25139185-25139199 chr6:25139177-25139198 chr6:25139188-25139201 chr6:25139189-25139199 chr6:25139182-25139193 chr6:25139188-25139199 chr6:25139181-25139192 chr6:25139187-25139201 chr6:25139187-25139198 chr6:25139182-25139195 chr6:25139182-25139195 chr6:25139181-25139201 chr6:25139182-25139195 chr6:25139187-25139200 chr6:25139183-25139193 chr6:25139182-25139196 chr6:25139183-25139200 chr6:25139186-25139200 chr6:25139188-25139200 chr6:25139189-25139203 chr6:25139182-25139195 chr6:25139179-25139193
8	IRF1	chr6:25139002-25139304	K562	blood:	n/a	chr6:25139183-25139197 chr6:25139185-25139199 chr6:25139177-25139198 chr6:25139188-25139201 chr6:25139189-25139199 chr6:25139182-25139193 chr6:25139188-25139199 chr6:25139181-25139192 chr6:25139187-25139201 chr6:25139187-25139198 chr6:25139182-25139195 chr6:25139182-25139195 chr6:25139181-25139201 chr6:25139182-25139195 chr6:25139187-25139200 chr6:25139183-25139193 chr6:25139182-25139196 chr6:25139183-25139200 chr6:25139186-25139200 chr6:25139188-25139200 chr6:25139189-25139203 chr6:25139182-25139195 chr6:25139179-25139193
9	STAT3	chr6:25138238-25139673	MCF10A-Er-Src	breast:	n/a	chr6:25139524-25139538 chr6:25139527-25139536 chr6:25139363-25139371 chr6:25139366-25139389 chr6:25139526-25139535 chr6:25139188-25139199 chr6:25138559-25138566 chr6:25139182-25139193
10	MAZ	chr6:25138151-25139330	GM12878	blood:	n/a	n/a
11	FOXM1	chr6:25138126-25139429	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:25137737-25139277	GM12892	blood:	n/a	n/a
13	RAD21	chr6:25138360-25139141	Hela-S3	cervix:	n/a	chr6:25138735-25138747
14	ATF2	chr6:25137739-25139485	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:25138286-25139307	MCF10A-Er-Src	breast:	n/a	n/a
16	PAX5	chr6:25138353-25139197	GM12878	blood:	n/a	chr6:25139184-25139193 chr6:25138559-25138568 chr6:25138579-25138588
17	MEF2A	chr6:25138776-25139401	GM12878	blood:	n/a	chr6:25139225-25139239 chr6:25139092-25139109
18	RELA	chr6:25137765-25139153	GM15510	blood:	n/a	n/a
19	SPI1	chr6:25137995-25139033	GM12878	blood:	n/a	chr6:25138561-25138568
20	CEBPB	chr6:25137782-25139143	IMR90	lung:	n/a	n/a
21	NFIC	chr6:25137751-25139570	GM12878	blood:	n/a	n/a
22	ZNF143	chr6:25138265-25139053	GM12878	blood:	n/a	n/a
23	TBP	chr6:25138232-25139305	GM12878	blood:	n/a	n/a
24	MTA3	chr6:25138119-25139367	GM12878	blood:	n/a	n/a
25	PBX3	chr6:25138291-25139154	SK-N-SH	brain:	n/a	n/a
26	MYC	chr6:25138447-25139263	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr6:25136835-25139403	GM12891	blood:	n/a	n/a
28	EP300	chr6:25138393-25139104	SK-N-SH_RA	brain:	n/a	n/a
29	CEBPB	chr6:25137713-25139611	GM12878	blood:	n/a	n/a
30	RELA	chr6:25137773-25139379	GM19099	blood:	n/a	n/a
31	FOS	chr6:25138194-25139210	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr6:25137453-25139116	GM12878	blood:	n/a	n/a
33	STAT5A	chr6:25138161-25139332	GM12878	blood:	n/a	chr6:25139188-25139199 chr6:25138559-25138566 chr6:25139182-25139193
34	FOXM1	chr6:25138117-25139412	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:25136992-25139613	MCF10A-Er-Src	breast:	n/a	n/a
36	ZNF384	chr6:25138440-25139201	GM12878	blood:	n/a	n/a
37	ATF2	chr6:25138138-25139054	GM12878	blood:	n/a	n/a
38	PAX5	chr6:25138694-25139226	GM12891	blood:	n/a	chr6:25139184-25139193
39	CEBPB	chr6:25137779-25139523	Hela-S3	cervix:	n/a	n/a
40	TBL1XR1	chr6:25138169-25139353	GM12878	blood:	n/a	n/a
41	RUNX3	chr6:25138167-25139298	GM12878	blood:	n/a	n/a
42	EP300	chr6:25138281-25139278	GM12878	blood:	n/a	chr6:25139184-25139198
43	RCOR1	chr6:25138324-25139461	GM12878	blood:	n/a	n/a
44	NFIC	chr6:25138231-25139234	SK-N-SH	brain:	n/a	n/a
45	BATF	chr6:25138903-25139261	GM12878	blood:	n/a	n/a
46	POU2F2	chr6:25138135-25139089	GM12878	blood:	n/a	n/a
47	FOS	chr6:25138220-25139218	MCF10A-Er-Src	breast:	n/a	n/a
48	EBF1	chr6:25138281-25139428	GM12878	blood:	n/a	n/a
49	PML	chr6:25137629-25139385	GM12878	blood:	n/a	chr6:25137823-25137831 chr6:25139267-25139275
50	FOS	chr6:25138726-25139177	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CMAHP	TF binding region
ENSG00000219682	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1002596	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs1547055	1.00[YRI][hapmap]
rs159988	0.88[JPT][hapmap]
rs167329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16890104	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1923195	0.89[CHD][hapmap]
rs2028973	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2166682	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2166683	0.88[JPT][hapmap]
rs2295737	1.00[YRI][hapmap]
rs2516577	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2894033	0.89[CHD][hapmap]
rs302966	0.88[JPT][hapmap]
rs302968	0.85[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302969	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302970	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302973	0.88[JPT][hapmap]
rs302976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs302980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs302982	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs302983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs302984	0.84[CHD][hapmap]
rs302986	0.86[AMR][1000 genomes]
rs302989	0.92[CHD][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs302990	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs302991	0.88[JPT][hapmap]
rs303006	0.88[JPT][hapmap]
rs303007	0.88[JPT][hapmap]
rs303008	0.88[JPT][hapmap]
rs303009	0.88[JPT][hapmap]
rs303015	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs303016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303017	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303019	0.89[MKK][hapmap]
rs303022	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs303023	0.93[AMR][1000 genomes]
rs303024	0.89[ASN][1000 genomes]
rs303025	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs303026	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3792970	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3792971	0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3792986	0.88[JPT][hapmap]
rs3812105	0.88[CHD][hapmap]
rs3818268	0.88[JPT][hapmap]
rs392852	0.88[JPT][hapmap]
rs456816	0.82[CHB][hapmap]
rs4711078	0.81[ASN][1000 genomes]
rs4712887	0.89[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs6906102	0.88[JPT][hapmap]
rs6919920	1.00[YRI][hapmap]
rs715426	0.88[JPT][hapmap]
rs9295646	0.80[CHD][hapmap]
rs9295647	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs9393613	1.00[YRI][hapmap]
rs9393617	0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1798120	chr6:25136860-25149538	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs303018	CMAH	cis	multi-tissue	Pritchard
rs303018	CMAH	cis	parietal	SCAN
rs303018	CMAH	cis	cerebellum	SCAN
rs303018	CMAH	cis	lymphoblastoid	seeQTL
rs303018	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs303018	SOX4	cis	parietal	SCAN
rs303018	LRRC16A	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25135200-25140200	Active TSS	Right Atrium	heart
2	chr6:25136000-25139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:25136200-25139600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr6:25136200-25139800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:25136200-25140000	Active TSS	Aorta	Aorta
6	chr6:25136400-25139200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr6:25136400-25139400	Active TSS	Brain Hippocampus Middle	brain
8	chr6:25136600-25139400	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr6:25136600-25139600	Active TSS	Duodenum Mucosa	Duodenum
10	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:25136800-25139400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr6:25136800-25139400	Active TSS	Brain Anterior Caudate	brain
13	chr6:25136800-25139400	Active TSS	Right Ventricle	heart
14	chr6:25136800-25140000	Active TSS	Ovary	ovary
15	chr6:25137000-25139400	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr6:25137000-25139400	Active TSS	Colonic Mucosa	Colon
17	chr6:25137000-25139400	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr6:25137000-25139800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:25137000-25140200	Active TSS	Psoas Muscle	Psoas
20	chr6:25137200-25139600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:25137200-25139600	Active TSS	Rectal Smooth Muscle	rectum
22	chr6:25137400-25139400	Active TSS	Primary T cells fromperipheralblood	blood
23	chr6:25137400-25139400	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr6:25137400-25139400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr6:25137400-25139400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr6:25137400-25139400	Active TSS	Colon Smooth Muscle	Colon
27	chr6:25137400-25139400	Active TSS	GM12878-XiMat	blood
28	chr6:25137400-25139600	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr6:25137600-25139400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:25137600-25139400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:25137600-25139400	Weak transcription	Fetal Heart	heart
32	chr6:25137600-25139600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:25137800-25139400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:25137800-25139600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:25137800-25139800	Active TSS	Brain Substantia Nigra	brain
36	chr6:25137800-25139800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr6:25137800-25139800	Flanking Active TSS	HUVEC	blood vessel
38	chr6:25138000-25139400	Active TSS	Fetal Kidney	kidney
39	chr6:25138000-25139600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:25138000-25139800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:25138000-25140200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:25138200-25139200	Active TSS	Primary B cells from peripheral blood	blood
43	chr6:25138200-25139400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:25138200-25139400	Active TSS	Brain Cingulate Gyrus	brain
45	chr6:25138200-25139400	Active TSS	Dnd41	blood
46	chr6:25138200-25139400	Active TSS	NHLF	lung
47	chr6:25138200-25139600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:25138200-25139600	Active TSS	Thymus	Thymus
49	chr6:25138200-25139600	Active TSS	NHDF-Ad	bronchial
50	chr6:25138400-25139200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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